From 2fd5b4cde4c0cf781595fa1ccd28658e1bea606d Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 15 Jul 2021 15:48:06 +0200
Subject: [PATCH] PDBize: do not put chains marked as 'polymer' in the ligand
chain.
---
CHANGELOG.txt | 4 +++-
modules/mol/alg/src/pdbize.cc | 4 +++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index c50db406f..56b2b050f 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -2,7 +2,9 @@ Changes in Release 2.2.x
--------------------------------------------------------------------------------
* Removed GUI components in containers
- * DSSP 4.0 support in DSSP binding (https://github.com/PDB-REDO/dssp)
+ * DSSP 4.0 support in DSSP binding (https://github.com/PDB-REDO/dssp)
+ * mol.alg.PDBize does not turn plain polymer chains (not marked peptide or
+ nucleotide) into ligand chains anymore
* Several minor bug fixes and improvements.
Changes in Release 2.2.0
diff --git a/modules/mol/alg/src/pdbize.cc b/modules/mol/alg/src/pdbize.cc
index c53749ff4..1c3c1c612 100644
--- a/modules/mol/alg/src/pdbize.cc
+++ b/modules/mol/alg/src/pdbize.cc
@@ -88,7 +88,9 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
if ((chain.IsPolypeptide() && chain_length >= peptide_min_size_) ||
(chain.IsPolynucleotide() && chain_length >= nucleicacid_min_size_) ||
((chain.IsOligosaccharide() || chain.IsPolysaccharide()) &&
- chain_length >= saccharide_min_size_)) {
+ chain_length >= saccharide_min_size_) ||
+ (chain.GetType() == CHAINTYPE_POLY && chain_length >= peptide_min_size_ &&
+ chain_length >= nucleicacid_min_size_)) {
if (*curr_chain_name_ == 0) {
throw std::runtime_error("running out of chain names");
}
--
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